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rdkit/Code/GraphMol/MolChemicalFeatures/testFeatures.cpp
Ricardo Rodriguez 7b7a8a4e17 Refactor iostreams includes (#8846) 
* refactor iostreams includes

* restore ostream to MonomerInfo.cpp
2025-10-08 16:08:01 +02:00

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// $Id$
//
// Copyright (C) 2004-2006 Rational Discovery LLC
//
// @@ All Rights Reserved @@
// This file is part of the RDKit.
// The contents are covered by the terms of the BSD license
// which is included in the file license.txt, found at the root
// of the RDKit source tree.
//
#include <RDGeneral/test.h>
#include <fstream>
#include <RDGeneral/Invariant.h>
#include <RDGeneral/RDLog.h>
#include <RDGeneral/utils.h>
#include <RDGeneral/StreamOps.h>
#include <sstream>
#include <boost/shared_ptr.hpp>
#include <GraphMol/RDKitBase.h>
#include <GraphMol/SmilesParse/SmilesParse.h>
#include <GraphMol/Substruct/SubstructMatch.h>
#include <GraphMol/MolChemicalFeatures/MolChemicalFeature.h>
#include <GraphMol/MolChemicalFeatures/MolChemicalFeatureDef.h>
#include <GraphMol/MolChemicalFeatures/MolChemicalFeatureFactory.h>
#include <GraphMol/MolChemicalFeatures/FeatureParser.h>
using namespace RDKit;
void test1() {
BOOST_LOG(rdErrorLog) << "-------------------------------------" << std::endl;
BOOST_LOG(rdErrorLog) << "AtomType parser testing." << std::endl;
std::string inLine;
std::map<std::string, std::string> atomTypeDefs;
atomTypeDefs.clear();
bool ok;
inLine = "AtomType donor [N,O]";
Local::parseAtomType(inLine, atomTypeDefs, 0);
TEST_ASSERT(atomTypeDefs.count("{donor}"));
TEST_ASSERT(!atomTypeDefs.count("{unsaturatedDonor}"));
TEST_ASSERT(atomTypeDefs["{donor}"] == "$([N,O])");
// check robustness to whitespace as we expand:
inLine = " AtomType donor\t[S]";
Local::parseAtomType(inLine, atomTypeDefs, 0);
TEST_ASSERT(atomTypeDefs.count("{donor}"));
TEST_ASSERT(!atomTypeDefs.count("{unsaturatedDonor}"));
TEST_ASSERT(atomTypeDefs["{donor}"] == "$([N,O,$([S])])");
inLine = "AtomType !donor [NH0]";
Local::parseAtomType(inLine, atomTypeDefs, 0);
TEST_ASSERT(atomTypeDefs.count("{donor}"));
TEST_ASSERT(!atomTypeDefs.count("{unsaturatedDonor}"));
TEST_ASSERT(atomTypeDefs["{donor}"] == "$([!$([NH0]);N,O,$([S])])");
inLine = "AtomType unsaturatedDonor [$([{donor}]!-[*])]";
Local::parseAtomType(inLine, atomTypeDefs, 0);
TEST_ASSERT(atomTypeDefs.count("{donor}"));
TEST_ASSERT(atomTypeDefs.count("{unsaturatedDonor}"));
TEST_ASSERT(atomTypeDefs["{donor}"] == "$([!$([NH0]);N,O,$([S])])");
TEST_ASSERT(atomTypeDefs["{unsaturatedDonor}"] ==
"$([$([$([!$([NH0]);N,O,$([S])])]!-[*])])");
ok = false;
try {
inLine = "";
Local::parseAtomType(inLine, atomTypeDefs, 0);
} catch (FeatureFileParseException &fpe) {
ok = true;
TEST_ASSERT(fpe.lineNo() == 0);
}
CHECK_INVARIANT(ok, "expected parse failure did not happen");
ok = false;
try {
inLine = "AtomTyped donor [N,O]";
Local::parseAtomType(inLine, atomTypeDefs, 0);
} catch (FeatureFileParseException &fpe) {
ok = true;
TEST_ASSERT(fpe.lineNo() == 0);
}
CHECK_INVARIANT(ok, "expected parse failure did not happen");
ok = false;
try {
inLine = "AtomType";
Local::parseAtomType(inLine, atomTypeDefs, 0);
} catch (FeatureFileParseException &fpe) {
ok = true;
TEST_ASSERT(fpe.lineNo() == 0);
}
CHECK_INVARIANT(ok, "expected parse failure did not happen");
ok = false;
try {
inLine = "AtomType donor";
Local::parseAtomType(inLine, atomTypeDefs, 0);
} catch (FeatureFileParseException &fpe) {
ok = true;
TEST_ASSERT(fpe.lineNo() == 0);
}
CHECK_INVARIANT(ok, "expected parse failure did not happen");
ok = false;
try {
inLine = "AtomType donor [N,O";
Local::parseAtomType(inLine, atomTypeDefs, 0);
} catch (FeatureFileParseException &fpe) {
ok = true;
TEST_ASSERT(fpe.lineNo() == 0);
}
CHECK_INVARIANT(ok, "expected parse failure did not happen");
BOOST_LOG(rdErrorLog) << " done" << std::endl;
}
void test2() {
BOOST_LOG(rdErrorLog) << "-------------------------------------" << std::endl;
BOOST_LOG(rdErrorLog) << "FeatureDefinition parser testing." << std::endl;
std::string inText, inLine;
std::istringstream ss;
MolChemicalFeatureDef *featDef;
bool ok;
std::map<std::string, std::string> atomTypeDefs;
atomTypeDefs["{donor}"] = "$([O,N])";
inText =
"DefineFeature HDonor1 [O,N]\n"
" Family HDONOR\n"
" Weights 1.0\n"
"EndFeature\n";
ss.clear();
ss.str(inText);
inLine = RDKit::getLine(ss);
unsigned int tmpLine = 2;
featDef = Local::parseFeatureDef(ss, inLine, tmpLine, atomTypeDefs);
TEST_ASSERT(featDef);
TEST_ASSERT(featDef->getFamily() == "HDONOR");
TEST_ASSERT(featDef->getType() == "HDonor1");
TEST_ASSERT(featDef->getSmarts() == "[O,N]");
TEST_ASSERT(featDef->getNumWeights() == 1);
TEST_ASSERT(feq(*featDef->beginWeights(), 1.0));
delete featDef;
inText =
"DefineFeature HDonor1 [{donor}]\n"
" Family HDONOR\n"
" Weights 2.0\n"
"EndFeature\n";
ss.clear();
ss.str(inText);
inLine = RDKit::getLine(ss);
featDef = Local::parseFeatureDef(ss, inLine, tmpLine, atomTypeDefs);
TEST_ASSERT(featDef);
TEST_ASSERT(featDef->getFamily() == "HDONOR");
TEST_ASSERT(featDef->getType() == "HDonor1");
TEST_ASSERT(featDef->getSmarts() == "[$([O,N])]");
TEST_ASSERT(featDef->getNumWeights() == 1);
TEST_ASSERT(feq(*featDef->beginWeights(), 1.0));
delete featDef;
inText =
"DefineFeature HDonorPair [{donor}][{donor}]\n"
" Family HDONOR\n"
" Weights 1.0,1\n"
"EndFeature\n";
ss.clear();
ss.str(inText);
inLine = RDKit::getLine(ss);
featDef = Local::parseFeatureDef(ss, inLine, tmpLine, atomTypeDefs);
TEST_ASSERT(featDef);
TEST_ASSERT(featDef->getFamily() == "HDONOR");
TEST_ASSERT(featDef->getType() == "HDonorPair");
TEST_ASSERT(featDef->getSmarts() == "[$([O,N])][$([O,N])]");
TEST_ASSERT(featDef->getNumWeights() == 2);
TEST_ASSERT(feq(*featDef->beginWeights(), 0.5));
TEST_ASSERT(feq(*++(featDef->beginWeights()), 0.5));
delete featDef;
ok = false;
inText =
"DefineFeature HDonor1 [{donor}]\n"
" Family HDONOR\n"
" Weights 1.0\n";
ss.clear();
ss.str(inText);
inLine = RDKit::getLine(ss);
try {
featDef = Local::parseFeatureDef(ss, inLine, tmpLine, atomTypeDefs);
} catch (FeatureFileParseException &) {
ok = true;
}
CHECK_INVARIANT(ok, "expected parse failure did not happen");
ok = false;
inText =
"DefineFeature HDonor1 [{donor}]\n"
"EndFeature\n";
ss.clear();
ss.str(inText);
inLine = RDKit::getLine(ss);
try {
featDef = Local::parseFeatureDef(ss, inLine, tmpLine, atomTypeDefs);
} catch (FeatureFileParseException &) {
ok = true;
}
CHECK_INVARIANT(ok, "expected parse failure did not happen");
BOOST_LOG(rdErrorLog) << " done" << std::endl;
}
void test3() {
BOOST_LOG(rdErrorLog) << "-------------------------------------" << std::endl;
BOOST_LOG(rdErrorLog) << "Test pulling feat defs from a string." << std::endl;
// std::string pathName=getenv("RDBASE");
// pathName +=
// "/Code/GraphMol/MolChemicalFeatures/test_data/smallsample.feats";
std::string inText, inLine;
std::istringstream ss;
int res;
MolChemicalFeatureDef::CollectionType featureDefs;
inText =
"AtomType donor [N,O]\n"
"AtomType !donor [H0]\n"
"DefineFeature HDonor1 [{donor}]\n"
" Family HBondDonor\n"
" Weights 1.0\n"
"EndFeature\n";
res = parseFeatureData(inText, featureDefs);
TEST_ASSERT(!res);
TEST_ASSERT(featureDefs.size() == 1);
TEST_ASSERT((*featureDefs.begin())->getSmarts() == "[$([!$([H0]);N,O])]");
BOOST_LOG(rdErrorLog) << " done" << std::endl;
}
void test4() {
BOOST_LOG(rdErrorLog) << "-------------------------------------" << std::endl;
BOOST_LOG(rdErrorLog) << "FeatureDef functionality testing." << std::endl;
ROMol *testMol;
MatchVectType mv;
std::string inText;
int res;
MolChemicalFeatureDef::CollectionType featureDefs;
MolChemicalFeatureDef::CollectionType::const_iterator featDefIt;
MolChemicalFeatureDef::CollectionType::value_type featDef;
inText =
"DefineFeature HDonor1 [N,O;!H0]\n"
" Family HBondDonor\n"
" Weights 1.0\n"
"EndFeature\n"
"DefineFeature HAcceptor1 [N,O]\n"
" Family HAcceptor\n"
" Weights 1.0\n"
"EndFeature\n";
res = parseFeatureData(inText, featureDefs);
TEST_ASSERT(!res);
TEST_ASSERT(featureDefs.size() == 2);
featDefIt = featureDefs.begin();
featDef = *featDefIt;
TEST_ASSERT(featDef->getSmarts() == "[N,O;!H0]");
TEST_ASSERT(featDef->getPattern());
TEST_ASSERT(featDef->getPattern()->getNumAtoms() == 1);
TEST_ASSERT(featDef->getNumWeights() == 1);
featDef = *(++featureDefs.begin());
TEST_ASSERT(featDef->getSmarts() == "[N,O]");
TEST_ASSERT(featDef->getPattern());
TEST_ASSERT(featDef->getPattern()->getNumAtoms() == 1);
TEST_ASSERT(featDef->getNumWeights() == 1);
testMol = SmilesToMol("COCN");
TEST_ASSERT(testMol);
featDef = *featureDefs.begin();
TEST_ASSERT(SubstructMatch(*testMol, *featDef->getPattern(), mv));
TEST_ASSERT(mv.size() == 1);
TEST_ASSERT(mv[0].first == 0);
TEST_ASSERT(mv[0].second == 3);
featDef = *(++featureDefs.begin());
TEST_ASSERT(SubstructMatch(*testMol, *featDef->getPattern(), mv));
TEST_ASSERT(mv.size() == 1);
TEST_ASSERT(mv[0].first == 0);
TEST_ASSERT(mv[0].second == 1 || mv[0].second == 3);
delete testMol;
BOOST_LOG(rdErrorLog) << " done" << std::endl;
}
void test5() {
BOOST_LOG(rdErrorLog) << "-------------------------------------" << std::endl;
BOOST_LOG(rdErrorLog) << "FeatureFactory testing." << std::endl;
ROMol *testMol;
MatchVectType mv;
std::string inText;
FeatSPtrList featSPtrs;
boost::shared_ptr<MolChemicalFeature> featSPtr;
MolChemicalFeatureFactory *factory;
MolChemicalFeatureDef::CollectionType::value_type featDef;
inText =
"DefineFeature HDonor1 [N,O;!H0]\n"
" Family HBondDonor\n"
" Weights 1.0\n"
"EndFeature\n"
"DefineFeature HAcceptor1 [N,O]\n"
" Family HBondAcceptor\n"
" Weights 1.0\n"
"EndFeature\n";
factory = buildFeatureFactory(inText);
TEST_ASSERT(factory);
TEST_ASSERT(factory->getNumFeatureDefs() == 2);
testMol = SmilesToMol("COCN");
TEST_ASSERT(testMol);
featDef = *factory->beginFeatureDefs();
TEST_ASSERT(SubstructMatch(*testMol, *featDef->getPattern(), mv));
BOOST_LOG(rdErrorLog) << "1" << std::endl;
TEST_ASSERT(mv.size() == 1);
TEST_ASSERT(mv[0].first == 0);
TEST_ASSERT(mv[0].second == 3);
featDef = *(++factory->beginFeatureDefs());
TEST_ASSERT(SubstructMatch(*testMol, *featDef->getPattern(), mv));
BOOST_LOG(rdErrorLog) << "2" << std::endl;
TEST_ASSERT(mv.size() == 1);
TEST_ASSERT(mv[0].first == 0);
TEST_ASSERT(mv[0].second == 1 || mv[0].second == 3);
// Test using the factory to find features:
featSPtrs = factory->getFeaturesForMol(*testMol);
BOOST_LOG(rdErrorLog) << "3" << std::endl;
TEST_ASSERT(featSPtrs.size() == 3);
featSPtr = *featSPtrs.begin();
TEST_ASSERT(featSPtr->getFamily() == "HBondDonor");
TEST_ASSERT(featSPtr->getType() == "HDonor1");
featSPtr = *(++featSPtrs.begin());
TEST_ASSERT(featSPtr->getFamily() == "HBondAcceptor");
TEST_ASSERT(featSPtr->getType() == "HAcceptor1");
featSPtr = *(++featSPtrs.begin());
TEST_ASSERT(featSPtr->getFamily() == "HBondAcceptor");
TEST_ASSERT(featSPtr->getType() == "HAcceptor1");
// Test limiting stuff with includeOnly
featSPtrs = factory->getFeaturesForMol(*testMol, "HBondAcceptor");
BOOST_LOG(rdErrorLog) << "4" << std::endl;
TEST_ASSERT(featSPtrs.size() == 2);
featSPtr = *featSPtrs.begin();
TEST_ASSERT(featSPtr->getFamily() == "HBondAcceptor");
TEST_ASSERT(featSPtr->getType() == "HAcceptor1");
featSPtr = *(++featSPtrs.begin());
TEST_ASSERT(featSPtr->getFamily() == "HBondAcceptor");
TEST_ASSERT(featSPtr->getType() == "HAcceptor1");
featSPtrs = factory->getFeaturesForMol(*testMol, "HBondDonor");
BOOST_LOG(rdErrorLog) << "5" << std::endl;
TEST_ASSERT(featSPtrs.size() == 1);
featSPtr = *featSPtrs.begin();
TEST_ASSERT(featSPtr->getFamily() == "HBondDonor");
TEST_ASSERT(featSPtr->getType() == "HDonor1");
featSPtrs = factory->getFeaturesForMol(*testMol, "NotPresent");
BOOST_LOG(rdErrorLog) << "6" << std::endl;
TEST_ASSERT(featSPtrs.size() == 0);
delete testMol;
delete factory;
BOOST_LOG(rdErrorLog) << " done" << std::endl;
}
void test6() {
BOOST_LOG(rdErrorLog) << "-------------------------------------" << std::endl;
BOOST_LOG(rdErrorLog) << "Feature Location testing." << std::endl;
ROMol *testMol;
Conformer *conf;
std::string inText;
FeatSPtrList featSPtrs;
boost::shared_ptr<MolChemicalFeature> featSPtr;
MolChemicalFeatureFactory *factory;
MolChemicalFeatureDef::CollectionType::value_type featDef;
inText =
"DefineFeature HDonor1 [N,O;!H0]\n"
" Family HBondDonor\n"
" Weights 1.0\n"
"EndFeature\n"
"DefineFeature Carboxyl1 C(=O)[O;H1,-]\n"
" Family ZnBinder\n"
" Weights 1.0,1.0,1.0\n"
"EndFeature\n";
factory = buildFeatureFactory(inText);
TEST_ASSERT(factory);
TEST_ASSERT(factory->getNumFeatureDefs() == 2);
testMol = SmilesToMol("C(=O)O");
TEST_ASSERT(testMol);
conf = new Conformer(3);
testMol->addConformer(conf);
conf->setAtomPos(0, RDGeom::Point3D(0, 0, 0.0));
conf->setAtomPos(1, RDGeom::Point3D(1.2, 0, 0.0));
conf->setAtomPos(2, RDGeom::Point3D(0, 1.5, 0.0));
featSPtrs = factory->getFeaturesForMol(*testMol);
TEST_ASSERT(featSPtrs.size() == 2);
featSPtr = *featSPtrs.begin();
TEST_ASSERT(featSPtr->getFamily() == "HBondDonor");
TEST_ASSERT(featSPtr->getType() == "HDonor1");
TEST_ASSERT(feq(featSPtr->getPos().x, 0.0));
TEST_ASSERT(feq(featSPtr->getPos().y, 1.5));
TEST_ASSERT(feq(featSPtr->getPos().z, 0.0));
featSPtr = *(++featSPtrs.begin());
TEST_ASSERT(featSPtr->getFamily() == "ZnBinder");
TEST_ASSERT(featSPtr->getType() == "Carboxyl1");
TEST_ASSERT(feq(featSPtr->getPos().x, 0.4));
TEST_ASSERT(feq(featSPtr->getPos().y, 0.5));
TEST_ASSERT(feq(featSPtr->getPos().z, 0.0));
delete testMol;
delete factory;
BOOST_LOG(rdErrorLog) << " done" << std::endl;
}
void test7() {
BOOST_LOG(rdErrorLog) << "-------------------------------------" << std::endl;
BOOST_LOG(rdErrorLog) << "Test building a FeatureFactory from a file"
<< std::endl;
std::string rdbase = getenv("RDBASE");
std::string fName =
rdbase + "/Code/GraphMol/MolChemicalFeatures/test_data/featDef.txt";
MolChemicalFeatureFactory *factory;
MolChemicalFeatureDef::CollectionType::const_iterator featDefIt;
MolChemicalFeatureDef::CollectionType::value_type featDef;
std::ifstream inStream(fName.c_str());
TEST_ASSERT(inStream.is_open());
auto &instrm = static_cast<std::istream &>(inStream);
factory = buildFeatureFactory(instrm);
TEST_ASSERT(factory);
TEST_ASSERT(factory->getNumFeatureDefs() == 2);
featDefIt = factory->beginFeatureDefs();
featDef = *featDefIt;
TEST_ASSERT(featDef->getFamily() == "HBondDonor");
featDefIt++;
featDef = *featDefIt;
TEST_ASSERT(featDefIt != factory->endFeatureDefs());
TEST_ASSERT(featDef->getFamily() == "HBondAcceptor");
featDefIt++;
TEST_ASSERT(featDefIt == factory->endFeatureDefs());
delete (factory);
BOOST_LOG(rdErrorLog) << " done" << std::endl;
}
void testIssue224() {
BOOST_LOG(rdErrorLog) << "-------------------------------------" << std::endl;
BOOST_LOG(rdErrorLog) << "Testing Issue 224." << std::endl;
std::string inText, inLine;
std::istringstream ss;
MolChemicalFeatureDef *featDef;
std::map<std::string, std::string> atomTypeDefs;
atomTypeDefs["{donor}"] = "$([O,N])";
inText =
"\n"
"DefineFeature HDonor1 [O,N]\n"
" Family HDONOR\n"
" Weights 1.0\n"
"EndFeature\n";
ss.clear();
ss.str(inText);
inLine = RDKit::getLine(ss);
unsigned int tmpLine = 2;
featDef = Local::parseFeatureDef(ss, inLine, tmpLine, atomTypeDefs);
TEST_ASSERT(featDef);
TEST_ASSERT(featDef->getFamily() == "HDONOR");
TEST_ASSERT(featDef->getType() == "HDonor1");
TEST_ASSERT(featDef->getSmarts() == "[O,N]");
TEST_ASSERT(featDef->getNumWeights() == 1);
TEST_ASSERT(feq(*featDef->beginWeights(), 1.0));
delete featDef;
inText =
"\n"
"# comment, ignore me\n"
"DefineFeature HDonor1 [O,N]\n"
" \n"
" Family HDONOR\n"
" \n"
"# comment, ignore me\n"
" Weights 1.0\n"
"# comment, ignore me\n"
"EndFeature\n";
ss.clear();
ss.str(inText);
inLine = RDKit::getLine(ss);
featDef = Local::parseFeatureDef(ss, inLine, tmpLine, atomTypeDefs);
TEST_ASSERT(featDef);
TEST_ASSERT(featDef->getFamily() == "HDONOR");
TEST_ASSERT(featDef->getType() == "HDonor1");
TEST_ASSERT(featDef->getSmarts() == "[O,N]");
TEST_ASSERT(featDef->getNumWeights() == 1);
TEST_ASSERT(feq(*featDef->beginWeights(), 1.0));
delete featDef;
// repeat those tests using some continuation lines
// (Issue 346):
inText =
"\n"
"# comment, ignore me\n"
"DefineFeature HDonor1 \\\n"
" [O,N]\n"
" Family HDONOR\n"
" \n"
"# comment, ignore me\n"
" Weights 1.0\n"
"# comment, ignore me\n"
"EndFeature\n";
ss.clear();
ss.str(inText);
inLine = RDKit::getLine(ss);
featDef = Local::parseFeatureDef(ss, inLine, tmpLine, atomTypeDefs);
TEST_ASSERT(featDef);
TEST_ASSERT(featDef->getFamily() == "HDONOR");
TEST_ASSERT(featDef->getType() == "HDonor1");
TEST_ASSERT(featDef->getSmarts() == "[O,N]");
TEST_ASSERT(featDef->getNumWeights() == 1);
TEST_ASSERT(feq(*featDef->beginWeights(), 1.0));
delete featDef;
inText =
"\n"
"# comment, ignore me\n"
"DefineFeature HDonor1 \\\n"
"# comment, ignore me\n"
" [O,N]\n"
" Family \\\n"
"\tHDONOR\n"
"# comment, ignore me\n"
" Weights \\\n"
"1.0\n"
"# comment, ignore me\n"
"EndFeature\n";
ss.clear();
ss.str(inText);
inLine = RDKit::getLine(ss);
featDef = Local::parseFeatureDef(ss, inLine, tmpLine, atomTypeDefs);
TEST_ASSERT(featDef);
TEST_ASSERT(featDef->getFamily() == "HDONOR");
TEST_ASSERT(featDef->getType() == "HDonor1");
TEST_ASSERT(featDef->getSmarts() == "[O,N]");
TEST_ASSERT(featDef->getNumWeights() == 1);
TEST_ASSERT(feq(*featDef->beginWeights(), 1.0));
delete featDef;
BOOST_LOG(rdErrorLog) << " done" << std::endl;
}
void testIssue225() {
BOOST_LOG(rdErrorLog) << "-------------------------------------" << std::endl;
BOOST_LOG(rdErrorLog) << "Testing Issue 225." << std::endl;
MatchVectType mv;
std::string inText;
int res;
MolChemicalFeatureDef::CollectionType featureDefs;
MolChemicalFeatureDef::CollectionType::const_iterator featDefIt;
MolChemicalFeatureDef::CollectionType::value_type featDef;
inText =
"DefineFeature HDonor1 [N,O;!H0]\n"
" Family HBondDonor\n"
" Weights 1.0\n"
"EndFeature\n"
"\n"
"DefineFeature HAcceptor1 [N,O]\n"
" Family HAcceptor\n"
" Weights 1.0\n"
"EndFeature\n";
res = parseFeatureData(inText, featureDefs);
TEST_ASSERT(!res);
TEST_ASSERT(featureDefs.size() == 2);
featDefIt = featureDefs.begin();
featDef = *featDefIt;
TEST_ASSERT(featDef->getSmarts() == "[N,O;!H0]");
TEST_ASSERT(featDef->getPattern());
TEST_ASSERT(featDef->getPattern()->getNumAtoms() == 1);
TEST_ASSERT(featDef->getNumWeights() == 1);
featDef = *(++featureDefs.begin());
TEST_ASSERT(featDef->getSmarts() == "[N,O]");
TEST_ASSERT(featDef->getPattern());
TEST_ASSERT(featDef->getPattern()->getNumAtoms() == 1);
TEST_ASSERT(featDef->getNumWeights() == 1);
BOOST_LOG(rdErrorLog) << " done" << std::endl;
}
void testIssue346() {
BOOST_LOG(rdErrorLog) << "-------------------------------------" << std::endl;
BOOST_LOG(rdErrorLog) << "Test Issue346" << std::endl;
std::string rdbase = getenv("RDBASE");
std::string fName =
rdbase + "/Code/GraphMol/MolChemicalFeatures/test_data/featDef2.txt";
MolChemicalFeatureFactory *factory;
MolChemicalFeatureDef::CollectionType::const_iterator featDefIt;
MolChemicalFeatureDef::CollectionType::value_type featDef;
std::ifstream inStream(fName.c_str());
TEST_ASSERT(inStream.is_open());
auto &instrm = static_cast<std::istream &>(inStream);
factory = buildFeatureFactory(instrm);
TEST_ASSERT(factory);
TEST_ASSERT(factory->getNumFeatureDefs() == 2);
featDefIt = factory->beginFeatureDefs();
featDef = *featDefIt;
TEST_ASSERT(featDef->getFamily() == "HBondDonor");
featDefIt++;
featDef = *featDefIt;
TEST_ASSERT(featDefIt != factory->endFeatureDefs());
TEST_ASSERT(featDef->getFamily() == "HBondAcceptor");
featDefIt++;
TEST_ASSERT(featDefIt == factory->endFeatureDefs());
delete (factory);
BOOST_LOG(rdErrorLog) << " done" << std::endl;
}
void testIssue347() {
BOOST_LOG(rdErrorLog) << "-------------------------------------" << std::endl;
BOOST_LOG(rdErrorLog) << "Test Issue347" << std::endl;
ROMol *testMol;
MolChemicalFeatureFactory *factory;
MolChemicalFeatureDef::CollectionType::const_iterator featDefIt;
MolChemicalFeatureDef::CollectionType::value_type featDef;
FeatSPtrList featSPtrs;
boost::shared_ptr<MolChemicalFeature> featSPtr;
std::string fdef;
fdef =
"DefineFeature CTriplet [C][C][C]\n"
" Family LumpedHydrophobe\n"
" Weights 1.0,1.0,1.0\n"
"EndFeature\n"
"DefineFeature CPair [C][C]\n"
" Family LumpedHydrophobe\n"
" Weights 1.0,1.0\n"
"EndFeature\n";
factory = buildFeatureFactory(fdef);
TEST_ASSERT(factory);
TEST_ASSERT(factory->getNumFeatureDefs() == 2);
featDefIt = factory->beginFeatureDefs();
featDef = *featDefIt;
TEST_ASSERT(featDef->getFamily() == "LumpedHydrophobe");
featDefIt++;
featDef = *featDefIt;
TEST_ASSERT(featDef->getFamily() == "LumpedHydrophobe");
featDefIt++;
TEST_ASSERT(featDefIt == factory->endFeatureDefs());
testMol = SmilesToMol("CCC");
TEST_ASSERT(testMol);
featSPtrs = factory->getFeaturesForMol(*testMol);
TEST_ASSERT(featSPtrs.size() == 1);
featSPtr = *featSPtrs.begin();
TEST_ASSERT(featSPtr->getFamily() == "LumpedHydrophobe");
TEST_ASSERT(featSPtr->getType() == "CTriplet");
delete factory;
// now reverse the order and we should get two matches:
fdef =
"DefineFeature CPair [C][C]\n"
" Family LumpedHydrophobe\n"
" Weights 1.0,1.0\n"
"EndFeature\n"
"DefineFeature CTriplet [C][C][C]\n"
" Family LumpedHydrophobe\n"
" Weights 1.0,1.0,1.0\n"
"EndFeature\n";
factory = buildFeatureFactory(fdef);
TEST_ASSERT(factory);
TEST_ASSERT(factory->getNumFeatureDefs() == 2);
featDefIt = factory->beginFeatureDefs();
featDef = *featDefIt;
TEST_ASSERT(featDef->getFamily() == "LumpedHydrophobe");
featDefIt++;
featDef = *featDefIt;
TEST_ASSERT(featDef->getFamily() == "LumpedHydrophobe");
featDefIt++;
TEST_ASSERT(featDefIt == factory->endFeatureDefs());
featSPtrs = factory->getFeaturesForMol(*testMol);
TEST_ASSERT(featSPtrs.size() == 3);
featSPtr = *featSPtrs.begin();
TEST_ASSERT(featSPtr->getFamily() == "LumpedHydrophobe");
TEST_ASSERT(featSPtr->getType() == "CPair");
featSPtr = *(++featSPtrs.begin());
TEST_ASSERT(featSPtr->getFamily() == "LumpedHydrophobe");
TEST_ASSERT(featSPtr->getType() == "CPair");
featSPtr = *(++ ++featSPtrs.begin());
TEST_ASSERT(featSPtr->getFamily() == "LumpedHydrophobe");
TEST_ASSERT(featSPtr->getType() == "CTriplet");
delete factory;
delete testMol;
BOOST_LOG(rdErrorLog) << " done" << std::endl;
}
void testIssue348() {
BOOST_LOG(rdErrorLog) << "-------------------------------------" << std::endl;
BOOST_LOG(rdErrorLog) << "Testing Issue 348." << std::endl;
MatchVectType mv;
std::string inText;
int res;
(void)res; // unused in any test
MolChemicalFeatureDef::CollectionType featureDefs;
MolChemicalFeatureDef::CollectionType::const_iterator featDefIt;
MolChemicalFeatureDef::CollectionType::value_type featDef;
inText =
"DefineFeature CTriplet \\\n"
"[C][C][C]\n"
" Family LumpedHydrophobe\n"
" Weights 1.0,1.0,1.0\n"
"EndFeature\n"
"DefineFeature CTriplet [C[C]\n"
" Family LumpedHydrophobe\n"
" Weights 1.0,1.0\n"
"EndFeature\n";
bool ok;
try {
res = parseFeatureData(inText, featureDefs);
ok = false;
} catch (FeatureFileParseException &fpe) {
ok = true;
TEST_ASSERT(fpe.lineNo() == 6);
}
TEST_ASSERT(ok);
}
void testNestedAtomTypes() {
BOOST_LOG(rdErrorLog) << "-------------------------------------" << std::endl;
BOOST_LOG(rdErrorLog) << "Testing Nested AtomType definitions." << std::endl;
MatchVectType mv;
std::string inText;
int res;
MolChemicalFeatureDef::CollectionType featureDefs;
MolChemicalFeatureDef::CollectionType::const_iterator featDefIt;
MolChemicalFeatureDef::CollectionType::value_type featDef;
inText =
"AtomType Carbon_NonPolar [C;!$(C=[O,N,P,S]);!$(C#N)]\n"
"AtomType Hphobe [{Carbon_NonPolar},c]\n"
"AtomType RingHphobe [{Hphobe};R]\n"
"DefineFeature HP1 [{RingHphobe}]\n"
" Family Hydrophobe\n"
" Weights 1.0\n"
"EndFeature\n";
res = parseFeatureData(inText, featureDefs);
TEST_ASSERT(!res);
TEST_ASSERT(featureDefs.size() == 1);
std::cerr << (*featureDefs.begin())->getSmarts() << std::endl;
}
void testGithub252() {
BOOST_LOG(rdErrorLog) << "-------------------------------------" << std::endl;
BOOST_LOG(rdErrorLog) << "Testing Github Issue #252: crash when calling "
"getPos() with no conformer."
<< std::endl;
BOOST_LOG(rdErrorLog) << " expect a precondition failure message below"
<< std::endl;
ROMol *testMol;
MolChemicalFeatureFactory *factory;
FeatSPtrList featSPtrs;
boost::shared_ptr<MolChemicalFeature> featSPtr;
std::string fdef =
"DefineFeature CTriplet [C][C][C]\n"
" Family LumpedHydrophobe\n"
" Weights 1.0,1.0,1.0\n"
"EndFeature\n"
"DefineFeature CPair [C][C]\n"
" Family LumpedHydrophobe\n"
" Weights 1.0,1.0\n"
"EndFeature\n";
factory = buildFeatureFactory(fdef);
TEST_ASSERT(factory);
TEST_ASSERT(factory->getNumFeatureDefs() == 2);
testMol = SmilesToMol("CCC");
TEST_ASSERT(testMol);
featSPtrs = factory->getFeaturesForMol(*testMol);
TEST_ASSERT(featSPtrs.size() == 1);
featSPtr = *featSPtrs.begin();
TEST_ASSERT(featSPtr->getFamily() == "LumpedHydrophobe");
bool ok = false;
try {
featSPtr->getPos();
} catch (const Invar::Invariant &) {
ok = true;
}
delete factory;
delete testMol;
TEST_ASSERT(ok);
BOOST_LOG(rdErrorLog) << " Done" << std::endl;
}
void testGithub2077() {
BOOST_LOG(rdErrorLog) << "-------------------------------------" << std::endl;
BOOST_LOG(rdErrorLog) << "Testing github 2077: add confId argument to "
"MolChemicalFeatureFactor::getFeaturesForMol()"
<< std::endl;
ROMol *testMol;
Conformer *conf;
std::string inText;
FeatSPtrList featSPtrs;
boost::shared_ptr<MolChemicalFeature> featSPtr;
MolChemicalFeatureFactory *factory;
MolChemicalFeatureDef::CollectionType::value_type featDef;
inText =
"DefineFeature HDonor1 [N,O;!H0]\n"
" Family HBondDonor\n"
" Weights 1.0\n"
"EndFeature\n"
"DefineFeature Carboxyl1 C(=O)[O;H1,-]\n"
" Family ZnBinder\n"
" Weights 1.0,1.0,1.0\n"
"EndFeature\n";
factory = buildFeatureFactory(inText);
TEST_ASSERT(factory);
TEST_ASSERT(factory->getNumFeatureDefs() == 2);
testMol = SmilesToMol("C(=O)O");
TEST_ASSERT(testMol);
conf = new Conformer(3);
testMol->addConformer(conf, true);
conf->setAtomPos(0, RDGeom::Point3D(0, 0, 0.0));
conf->setAtomPos(1, RDGeom::Point3D(1.2, 0, 0.0));
conf->setAtomPos(2, RDGeom::Point3D(0, 1.5, 0.0));
conf = new Conformer(3);
testMol->addConformer(conf, true);
conf->setAtomPos(0, RDGeom::Point3D(1, 0, 0.0));
conf->setAtomPos(1, RDGeom::Point3D(2.2, 0, 0.0));
conf->setAtomPos(2, RDGeom::Point3D(1, 1.5, 0.0));
{
featSPtrs = factory->getFeaturesForMol(*testMol);
TEST_ASSERT(featSPtrs.size() == 2);
featSPtr = *featSPtrs.begin();
TEST_ASSERT(featSPtr->getActiveConformer() == -1);
TEST_ASSERT(featSPtr->getFamily() == "HBondDonor");
TEST_ASSERT(featSPtr->getType() == "HDonor1");
TEST_ASSERT(feq(featSPtr->getPos().x, 0.0));
TEST_ASSERT(feq(featSPtr->getPos().y, 1.5));
TEST_ASSERT(feq(featSPtr->getPos().z, 0.0));
}
{
featSPtrs = factory->getFeaturesForMol(*testMol, "", 1);
TEST_ASSERT(featSPtrs.size() == 2);
featSPtr = *featSPtrs.begin();
TEST_ASSERT(featSPtr->getActiveConformer() == 1);
TEST_ASSERT(featSPtr->getFamily() == "HBondDonor");
TEST_ASSERT(featSPtr->getType() == "HDonor1");
TEST_ASSERT(feq(featSPtr->getPos().x, 1.0));
TEST_ASSERT(feq(featSPtr->getPos().y, 1.5));
TEST_ASSERT(feq(featSPtr->getPos().z, 0.0));
}
delete testMol;
delete factory;
BOOST_LOG(rdErrorLog) << " done" << std::endl;
}
//-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*
//
//-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*
int main() {
RDLog::InitLogs();
#if 1
test1();
test2();
test3();
test4();
test5();
test6();
test7();
testIssue224();
testIssue225();
testIssue346();
testIssue347();
testIssue348();
#endif
testNestedAtomTypes();
testGithub252();
testGithub2077();
}
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